Import Images to new Wordpress site with folder hierarchy intact?

I created a new Wordpress site for someone, and exported all of their posts and pages from their old worpress site and then imported them to the new site. I did not consider the images, so when I put the new site up on the domain the images were broken. I had saved the entire old site files and database, so when I uploaded the missing images by uploading the wp-content/uploads/2010/... folders from the old site to the new site, the images were restored.

The problem is that now they do not appear in the Media Library on the new site. Is there a way to get them to appear and be accessible from there while maintaining the existing file structure?

The reason they don't appear in the media library is because you merely copied them into place instead of uploading them through the Media interface. The easiest fix is via a plugin:
http://wordpress.org/extend/plugins/add-from-server/

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